The vertical distribution characteristics of nitrogen, phosphorus and DOM in secondary effluent of soil infiltration WWTP were studied by 3D-EEMs and PARAFAC. The experiment was carried out on a pilot-scale soil infiltration system with a sampling port at 30 cm intervals from top to bottom. The collected samples were identified by PARAFAC model as having 4 fluorescent components at different points in the system, including two humus substances (C1, C2) and two protein substances (C3, C4) respectively. Fmax analysis showed that the tryptophan represented by C4 was more easily degraded than other three kinds of substances, that is, tryptophan was the most easily degraded, followed by fulvic acid, humic acid and protein-like substances. The Fmax variation of the four components was the largest at 0~30 cm, which showed that the biochemical reaction was the most intense and the migration and transformation rate of DOM was the highest. The source of DOM in soil infiltration system and the variation law of DOM in different depths could be revealed by means of PARAFAC, PCA and CA. Soil infiltration system was unfavorable for TN and nitrate removal in treating secondary effluent of sewage treatment plant under 4 L·d-1 low load condition. The subsequent denitrification processes such as denitrification filter could be coupled to enhance denitrification and nitrogen removal rate. The adsorption of phosphorus on soil had not yet reached saturation state, and had maintained a high TP removal efficiency.